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Looking to replace Scrappie with Squigulator in a signal generation pipeline, but getting warning from short sequences. Is there a solution besides padding the sequences with random/homopolymer sequen…
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Hello, I have a question, is possible polish the primary/alternate and haplo1/haplo2 with illumina reads?
Thanks so much.
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Dear developers,
I am currently working with miRNA-seq reads from Illumina platforms, whose length ranges roughly from 16 to 30 nucleotides.
Do you think bowtie can outperform other popular mapp…
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Thank you again for developing this great tool. We have a fish ONT dataset (10.4.1) which we assembled with nextdenovo to produce a genome size of ~560Mb and an N50=~7Mb.
I thought I should also try…
melop updated
1 month ago
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**Is your feature request related to a problem? Please describe.**
When users polish long read assemblies with short reads, they tend to believe that the new consensus is always better than the origi…
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### Ask away!
How would you recommend implementing the StringTie --mix parameter in the pipeline? (To use both short and long reads). I have the pipeline working on the cluster normally. I am wonderi…
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**Feature request**
An option that when polishing an assembly with short reads, all bases of an assembly that are not covered by at least X (user supplied parameter) reads are set to N, indicating th…
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So one common use with websockets is to exchange JSON docs back and forth. They are self delimiting, but doing byte-at-a-time parsing can be excruciatingly slow.
json.load does this:
```
return load…
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Dear @lfaino
Do you think it would be difficult to implement an option to use several bam files for short reads (many libs), instead of merging in a very huge file. Or another solution (very inter…
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Hi,
we want to analyze somatic mutations on ONT short reads (300-500bps).
You are filtering and removing variants that are close (100bp?, reported qual set to 0, filter: LowQual;ReadStartEnd)
to s…